Contacts of the helix formed by residues 170 - 187 (chain A) in PDB entry 2YZ2
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 170 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLY* 5.7 2.4 + - - -
168A GLY 4.1 1.2 + - - -
169A LEU* 1.3 72.6 - - - +
171A ARG* 1.3 61.5 + - + +
172A GLU* 3.8 17.0 + - - +
173A GLY* 3.3 17.3 + - - -
174A LYS* 2.8 36.3 + - - +
42B THR* 2.6 35.3 + - - +
196B HIS* 3.9 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ASP* 1.3 76.8 - - + +
172A GLU* 1.3 61.6 + - + +
174A LYS* 3.5 9.3 + - - +
175A THR* 2.9 32.4 + - + +
41B ASN* 4.0 21.2 - - - +
196B HIS* 4.0 28.6 + - - -
233B PHE* 3.5 68.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ASP* 3.3 16.0 + - - +
171A ARG* 1.3 76.9 - - + +
173A GLY* 1.4 63.7 + - - +
175A THR* 3.3 9.2 + - - +
176A ASP* 2.9 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLY* 4.6 15.0 - - - -
169A LEU* 4.0 18.2 - - - -
170A ASP* 3.3 15.9 + - - -
171A ARG 3.4 0.2 - - - -
172A GLU* 1.4 80.9 - - - +
174A LYS* 1.3 57.9 + - - +
176A ASP* 3.3 7.8 + - - +
177A LEU* 2.9 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 3.7 39.0 - - + -
169A LEU* 3.3 25.1 + - + +
170A ASP 2.8 22.4 - - - +
171A ARG* 3.6 9.1 - - - +
172A GLU 3.2 0.2 - - - -
173A GLY* 1.3 71.8 - - - +
175A THR* 1.3 67.8 + - + +
177A LEU* 3.0 8.1 + - - +
178A LEU* 2.9 34.8 + - + +
200A THR* 5.9 7.8 - - + +
196B HIS* 5.4 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ARG* 2.9 26.2 + - + +
172A GLU* 3.3 9.4 + - - +
174A LYS* 1.3 76.0 - - + +
176A ASP* 1.3 66.3 + - - +
178A LEU* 3.4 7.9 + - - +
179A ARG* 3.0 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ARG* 3.3 42.3 + - - +
172A GLU* 2.9 32.9 + - - +
173A GLY* 3.5 7.6 - - - +
175A THR* 1.3 81.7 + - - +
177A LEU* 1.3 65.7 + - - +
179A ARG* 3.4 9.5 + - - +
180A ILE* 3.3 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLY* 4.8 1.6 - - - +
145A ARG* 3.8 16.6 - - + -
146A ARG* 4.0 21.5 - - + -
149A ILE* 4.5 20.9 - - + -
162A LEU* 4.9 7.0 - - + -
165A PRO* 3.5 39.5 - - + +
166A LEU* 3.6 14.6 - - + -
169A LEU* 3.7 18.4 - - + -
173A GLY* 2.9 12.2 + - - +
174A LYS* 3.0 7.4 + - - +
176A ASP* 1.3 75.1 - - - +
178A LEU* 1.3 59.1 + - - +
180A ILE* 3.0 30.8 + - + +
181A VAL* 3.4 8.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PRO* 6.2 1.1 - - + -
166A LEU* 4.3 17.9 - - + -
174A LYS* 2.9 25.6 + - + +
175A THR* 4.0 6.7 - - - +
177A LEU* 1.3 75.7 - - - +
179A ARG* 1.3 61.7 + - - +
181A VAL* 3.1 16.9 + - + +
182A GLU* 3.1 27.0 + - - +
193A LEU* 5.2 2.2 - - + -
200A THR 4.2 10.1 - - - +
201A VAL* 4.0 24.5 - - + -
204A HIS* 3.6 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A THR 3.0 17.8 + - - +
176A ASP* 3.6 10.3 - - - +
177A LEU 3.2 0.2 - - - -
178A LEU* 1.3 73.8 - - - +
180A ILE* 1.3 64.4 + - + +
182A GLU* 3.4 10.1 + - - +
183A LYS* 3.1 66.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE* 3.9 20.5 - - + +
124A VAL* 3.7 30.1 - - + +
146A ARG* 3.6 31.9 - - + -
149A ILE* 4.2 23.8 - - + -
153A ILE* 5.6 0.7 - - + -
160A LEU* 4.8 11.4 - - + -
162A LEU* 5.9 2.0 - - + -
176A ASP 3.4 16.2 - - - +
177A LEU* 3.0 19.8 + - + +
179A ARG* 1.3 79.9 - - + +
181A VAL* 1.3 56.8 + - + +
183A LYS* 3.3 8.2 + - - +
184A TRP* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A CYS* 4.2 7.9 - - - -
160A LEU* 5.8 0.9 - - - -
162A LEU* 3.8 16.2 - - + -
165A PRO* 5.6 2.7 - - + -
177A LEU* 3.4 11.9 + - + +
178A LEU* 3.1 19.1 + - + +
180A ILE* 1.3 77.7 - - + +
182A GLU* 1.3 57.2 + - - +
184A TRP* 3.4 7.0 + - - +
185A LYS* 3.1 43.0 + - + +
191A VAL* 4.1 21.3 - - + +
193A LEU* 3.7 33.7 - - + -
204A HIS* 4.3 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU 3.1 17.6 + - - +
179A ARG* 3.8 13.7 - - - +
180A ILE 3.4 0.2 - - - -
181A VAL* 1.3 73.2 - - - +
183A LYS* 1.3 60.5 + - + +
185A LYS* 3.4 35.3 + - - +
186A THR* 2.8 35.2 + - - +
203A ASN 4.9 0.9 - - - +
204A HIS* 3.1 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU 3.7 14.1 + - - -
123A PHE* 3.1 52.7 + - + +
125A GLY* 4.9 3.4 - - - +
179A ARG* 3.1 58.0 + - + +
180A ILE* 3.6 8.1 - - + +
182A GLU* 1.3 73.6 - - - +
184A TRP* 1.3 68.1 + - - +
186A THR* 2.9 17.9 + - - -
187A LEU* 3.1 14.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE* 3.6 33.5 - + - -
153A ILE* 3.5 37.2 - - + -
156A GLU* 4.9 0.7 - - - -
157A PRO* 3.2 35.7 - - + -
158A ASP 4.0 1.1 + - - -
159A ILE 4.0 2.5 - - - -
160A LEU* 3.6 35.3 - - + +
180A ILE 2.9 17.2 + - - +
181A VAL* 3.6 7.9 - - - +
183A LYS* 1.3 78.3 - - - +
185A LYS* 1.3 61.8 + - - +
187A LEU* 3.1 17.4 + - + +
189A LYS* 3.3 53.9 + - + +
190A THR 2.9 27.9 + - - -
191A VAL* 3.7 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY 5.3 5.6 - - - +
35A CYS* 3.4 32.4 - - + +
181A VAL* 3.1 22.1 + - + +
182A GLU* 3.4 28.6 + - - +
183A LYS 3.1 0.4 - - - -
184A TRP* 1.3 72.3 - - - +
186A THR* 1.3 61.7 + - - +
187A LEU 3.0 2.0 - - - -
188A GLY* 2.8 20.6 + - - -
189A LYS 4.1 9.4 - - - +
191A VAL* 3.6 16.4 - - + -
203A ASN 5.4 0.6 + - - -
204A HIS* 3.0 24.6 + - - +
205A VAL* 4.7 1.6 - - - +
206A ASP* 4.8 9.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A GLU* 2.8 23.0 + - - +
183A LYS* 2.9 9.9 + - - -
185A LYS* 1.3 76.2 - - - +
187A LEU* 1.3 65.0 + - + +
188A GLY* 3.1 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE* 3.4 35.9 - - + -
183A LYS* 3.1 10.5 + - + +
184A TRP* 3.4 10.1 - - + +
185A LYS 3.0 0.4 - - - -
186A THR* 1.3 81.5 - - + +
188A GLY* 1.3 59.1 + - - +
189A LYS* 3.3 27.6 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il